Computational study on the impact of linkage sequence on the structure and dynamics of lignin.

Lignin, one of the most abundant biopolymers on Earth, is of great research interest due to its industrial applications including biofuel production and materials science. The structural composition of lignin plays an important role in shaping its properties and functionalities. Notably, lignin exhibits substantial compositional diversity, which varies not only between different plant species but even within the same plant.

Water molecule ordering on the surface of an intrinsically disordered protein.

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation.

Dynamics of the lignin glass transition.

The dynamics of lignin, a complex and heterogeneous major plant cell-wall macromolecule, is of both fundamental and practical importance. Lignin is typically heated to temperatures above its glass transition to facilitate its industrial processing. We performed molecular dynamics simulations to investigate the segmental (α) relaxation of lignin, the dynamical process that gives rise to the glass transition.

Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins.

Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected.

Quasielastic neutron scattering in biology: Theory and applications.

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted.

Motional displacements in proteins: The origin of wave-vector-dependent values.

The average mean-square displacement, 〈r(2)〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r(2)〉 is obtained from the observed elastic incoherent dynamic structure factor, S(i)(Q,ω=0), assuming the form S(i)(Q,ω=0) =exp(-Q(2)〈r(2)〉/3). This is often referred to as the Gaussian approximation (GA) to S(i)(Q,ω=0).

Long-time mean-square displacements in proteins.

We propose a method for obtaining the intrinsic, long-time mean square displacement (MSD) of atoms and molecules in proteins from finite-time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns, and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, I(inc)(Q,t), for finite times.

Intrinsic mean-square displacements in proteins.

The thermal mean-square displacement (MSD) of hydrogen in proteins and its associated hydration water is measured by neutron scattering experiments and used an indicator of protein function. The observed MSD as currently determined depends on the energy resolution width of the neutron scattering instrument employed. We propose a method for obtaining the intrinsic MSD of H in the proteins, one that is independent of the instrument resolution width.

Vibrational dynamics of hydrogen in proteins.

Biological macromolecules expand with increasing temperature and this dynamic expansion is associated with the onset of function. The expansion is typically characterized by the mean square vibrational displacement (MSD), of specific constituents such as hydrogen within the macromolecules. The increases with increasing temperature and the slope of versus temperature can increase significantly at a temperature T{D} identified as a dynamical transition.